Fix clever vcf header and add sorting step

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/CleverFixVCF.scala

@@ -81,6 +81,7 @@ object CleverFixVCF extends ToolCommand {
 ##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakends">
 ##INFO=<ID=PARID,Number=1,Type=String,Description="ID of partner breakend">
 ##INFO=<ID=EVENT,Number=1,Type=String,Description="ID of event associated to breakend">
+##INFO=<ID=BPWINDOW,Number=2,Type=Integer,Description="Window of breakpoints">
 ##INFO=<ID=CILEN,Number=2,Type=Integer,Description="Confidence interval around the inserted material between breakends">
 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Read Depth of segment containing breakend">
 ##INFO=<ID=DPADJ,Number=.,Type=Integer,Description="Read Depth of adjacency">

public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Clever.scala

@@ -15,7 +15,8 @@
  */
 package nl.lumc.sasc.biopet.pipelines.shiva.svcallers
 
-import nl.lumc.sasc.biopet.extensions.clever.{ CleverCaller, CleverFixVCF }
+import nl.lumc.sasc.biopet.extensions.clever.{CleverCaller, CleverFixVCF}
+import nl.lumc.sasc.biopet.extensions.picard.SortVcf
 import nl.lumc.sasc.biopet.utils.config.Configurable
 
 /** Script for sv caler Clever */
@@ -31,11 +32,17 @@ class Clever(val root: Configurable) extends SvCaller {
 
       val cleverVCF = new CleverFixVCF(this)
       cleverVCF.input = clever.outputvcf
-      cleverVCF.output = new File(cleverDir, s"${sample}.clever.vcf")
+      cleverVCF.output = new File(cleverDir, s".${sample}.clever.vcf")
       cleverVCF.sampleName = sample
+      cleverVCF.isIntermediate = true
       add(cleverVCF)
 
-      addVCF(sample, cleverVCF.output)
+      val sortvcf = new SortVcf(this)
+      sortvcf.input = cleverVCF.output
+      sortvcf.output = new File(cleverDir, s"${sample}.clever.vcf")
+      add(sortvcf)
+
+      addVCF(sample, sortvcf.output)
     }
   }
 }